Variant report

Variant	rs3117292
Chromosome Location	chr6:29652199-29652200
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:29637497..29639601-chr6:29651008..29653048,2	K562	blood:

Variant related genes	Relation type
ENSG00000204655	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1018935	0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2535235	0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2535236	0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2747434	0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2747436	0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2747442	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2747443	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2982839	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3095286	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3095288	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3095289	0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3117291	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs3117293	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3117294	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3129045	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3129053	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3129054	0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3129057	0.82[AFR][1000 genomes]
rs3131847	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs385354	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs430133	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758039	chr6:29469101-29672665	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	esv2759411	chr6:29469101-29672665	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv883530	chr6:29645038-29677641	Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv10808	chr6:29648051-29653183	Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3117292	C6orf12	Cis_1M	lymphoblastoid	RTeQTL
rs3117292	ZNF323	cis	parietal	SCAN
rs3117292	CHFR	trans	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29625000-29663600	Weak transcription	Right Atrium	heart
2	chr6:29648800-29662600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr6:29649200-29655000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr6:29651200-29652200	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr6:29651400-29652200	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr6:29651400-29652200	Enhancers	H1 Cell Line	embryonic stem cell
7	chr6:29651400-29652200	Enhancers	H9 Cell Line	embryonic stem cell
8	chr6:29651400-29652200	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr6:29651400-29652200	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr6:29651400-29652200	Enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr6:29651400-29652200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr6:29651400-29652400	Enhancers	iPS-15b Cell Line	embryonic stem cell
13	chr6:29651400-29652400	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr6:29651600-29652200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
15	chr6:29651600-29652200	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr6:29651600-29652200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr6:29651800-29652200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr6:29652000-29652200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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